while we are all debating Jonathan's motives in MOS, let's remember what Snyder said when Costner was 1st cast in the role.

“Jonathan Kent is the only father figure Clark has ever had, the man who was there to help Clark understand what he was meant to do in the world as Superman,” said Snyder in a statement. “Kevin will be able to communicate the quiet strength of this rural American man who raised the greatest super hero of all time.”

so, it seems ( and I hope so ) that there is more to Costner's Jonathan than just the "fearful, overprotective father."